GEO Accession viewer

NCBI > GEO > Accession Display

Not logged in | Login

GEO help: Mouse over screen elements for information.

Sample GSM1197192

Query DataSets for GSM1197192

Status

Public on Sep 15, 2013

Title

pHAN_DRR1.2_RNAseq

Sample type

SRA

Source name

C2C12

Organism

Mus musculus

Characteristics

strain: C3H
developmental stage: 4hrs differentiating Myocytes
chip antibody: none

Treatment protocol

For differentiation, cells were placed in media containing Dulbecco's Modified Eagle Medium (DMEM) supplemented with 2% horse serum, penicillin/streptomycin and insulin-Transferrin-selenium-A.

Growth protocol

C2C12 myoblasts were routinely grown in Dulbecco's Modified Eagle Medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and penicillin/streptomycin.

Extracted molecule

polyA RNA

Extraction protocol

For ChIP-Seq, lysates were cleared from sonicated nuclei and used for immunoprecipitation. For RNA-Seq, RNA was extracted according to TRIzol protocol (invitrogen).
For ChIPSeq, cells were cross-linked in 1% formaldehyde and processed according to Mousavi et al. 2012. Purified DNA was processed according to manufacturer's protocol. For polyA RNA-Seq, Illumina protocol was followed. For ribosomal depletion, ribo-zero was used (epicenter).

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina Genome Analyzer IIx

Description

PolyA RNA sequencing
Processed data file 'PhanDRR1.2_PhanGFP_cds_exp.diff.txt' is linked as a supplementary file on the Series record.

Data processing

Illumina Casava1.8 software used for basecalling.
Sequenced reads were mapped to mm9 whole genome using illumina pipline (Eland) , and TopHat(Trapnell C, et.al 2009) for RNA-Seq
MyoD and MyoG Peaks were called using MACS ( Zhang et al, 2008), with pvalue of 10^-6, --gsize mm, and the rest were default setting. H3k4me1 peaks were called using SICER Algorithm ( Zang et al, 2009) with the following setting: window size (200bp), window pvalue (0.2), gap size(600bp) and the FDR of 0.05
Genome_build: mm9
Supplementary_files_format_and_content: ChIP-Seq: peak files in bed formats and wig files were generated using filtered reads residing in enriched regions
Supplementary_files_format_and_content: RNA-Seq: txt files represent FPKM(RPKM) and differential expression analysis

Submission date

Jul 29, 2013

Last update date

May 15, 2019

Contact name

Hossein Zare

E-mail(s)

hzare@mail.nih.gov

Organization name

NIH

Street address

5o South Dr #1347